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10.1101/2024.11.08.622131 | Cell fate determination is associated with changes in competing transcriptional units in the human GATA1 and GATA2 lineage-determining transcription factors | Anderson, E. M.; Li, H.; Ruesch, M.; Wright, P. W.; Freud, A. G.; Anderson, S. K. | Stephen K Anderson | National Cancer Institute | 2024-11-09 | 1 | new results | cc_no | developmental biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622131.source.xml | The GATA1 and GATA2 transcription factors play a central role in early cell fate decisions in hematopoietic progenitor cells. Although the switch from GATA2 to GATA1 occupancy at GATA-binding sites in erythroblast-specific genes has been extensively studied, the underlying molecular mechanisms controlling this switch a... | null | biorxiv |
10.1101/2024.11.08.622587 | A comprehensive representation of selection at loci with multiple alleles that allows complex forms of genotypic fitness | Vellnow, N.; Gossmann, T. I.; Waxman, D. | Toni Ingolf Gossmann | TU Dortmund University | 2024-11-09 | 1 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622587.source.xml | Genetic diversity is central to the process of evolution. Both natural selection and random genetic drift are influenced by the level of genetic diversity of a population; selection acts on diversity while drift samples from it. At a given locus in a diploid population, each individual carries only two alleles, but the... | null | biorxiv |
10.1101/2024.11.08.622694 | Small molecule oxybutynin rescues proliferative capacity of complex III-defective MPCs | Qu, Y.; Edwards, K.; Li, M.; Liu, Y.; Tsai, P.-Y.; Cheng, C.; Blum, J.; Acor, N.; Oshoe, T.; Rooney, K.; Walter, C.; Thirumlaikumar, V. P.; Thalacker-Mercer, A.; Skirycz, A.; Barrow, J. | Joeva Barrow | Cornell University | 2024-11-09 | 1 | new results | cc_no | cell biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622694.source.xml | Mitochondrial disease encompasses a group of genetically inherited disorders hallmarked by an inability of the respiratory chain to produce sufficient ATP. These disorders present with multisystemic pathologies that predominantly impact highly energetic tissues such as skeletal muscle. There is no cure or effective tre... | null | biorxiv |
10.1101/2024.11.08.622727 | Challenges in inferring breathing rhythms from olfactory bulb local field potentials | Rafilson, S. E.; Hess, N.; Findley, T. M.; Smear, M. | Matt Smear | University of Oregon | 2024-11-09 | 1 | new results | cc_by_nc | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622727.source.xml | Odors convey useful navigational and episodic information, yet much of the chemical world remains inaccessible without active sampling through sniffing. To effectively interpret olfactory cues, the brain must unify odor-driven activity with respiratory cycles, making accurate respiratory measurements critical in unders... | null | biorxiv |
10.1101/2024.11.08.622735 | Targeting Corticotropin-Releasing Hormone Receptor Type 1 (CRHR1) Neurons: Validating the Specificity of a Novel Transgenic Crhr1-FlpO Mouse | Hardy, M.; Chen, Y.; Baram, T. Z.; Justice, N. J. | Tallie Z Baram | University of California Irvine | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622735.source.xml | Introduction: Corticotropin-releasing hormone (CRH) signaling through its cognate receptors, CRHR1 and CRHR2, contributes to diverse stress-related functions in the mammalian brain. Whereas CRHR2 is predominantly expressed in choroid plexus and blood vessels, CRHR1 is abundantly expressed in neurons in discrete brain r... | null | biorxiv |
10.1101/2024.11.08.622712 | Projections between the globus pallidus externa and cortex span motor and non-motor regions | Ferenczi, E. A.; Wang, W.; Biswas, A.; Pottala, T.; Dong, Y.; Chan, A. K.; Albanese, M. A.; Sohur, R. S.; Jia, T.; Mastro, K. J.; Sabatini, B. L. | Bernardo L Sabatini | Howard Hughes Medical Institute, Harvard Medical School | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622712.source.xml | The globus pallidus externa (GPe) is a heterogenous nucleus of the basal ganglia, with intricate connections to other basal ganglia nuclei, as well as direct connections to the cortex. The anatomic, molecular and electrophysiologic properties of cortex-projecting pallidocortical neurons are not well characterized. Here... | null | biorxiv |
10.1101/2024.11.09.622790 | Encoding opposing valences through frequency-dependent transmitter switching in single peptidergic neurons | Kim, D.-I.; Kang, S. J.; Jhang, J.; Jo, Y. S.; Park, S.; Ye, M.; Pyeon, G. H.; Im, G.-H.; Kim, S.-G.; Han, S. | Sung Han | The Salk Institute for Biological Studies | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622790.source.xml | Peptidergic neurons often co-express fast transmitters and neuropeptides in separate vesicles with distinct release properties. However, the release dynamics of each transmitter in various contexts have not been fully understood in behaving animals. Here, we demonstrate that calcitonin gene-related peptide (CGRP) neuro... | null | biorxiv |
10.1101/2024.11.08.622738 | Bichromatic exon-reporters reveal voltage-gated Ca2+-channel splice-isoform diversity across Drosophila neurons in vivo | Macleod, G. T.; Feghhi, T.; Hernandez, R.; Oliva, C. D.; Mahneva, O. | Gregory T Macleod | Tulane University | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622738.source.xml | Every neuron contains the same genomic information but its complement of proteins is the product of countless neuron-specific steps including pre-mRNA splicing. Despite advances in RNA sequencing techniques, pre-mRNA splicing biases that favor one isoform over another are largely inscrutable in live neurons in situ. He... | null | biorxiv |
10.1101/2024.11.08.622698 | Alternative EEG pre-processing pipelines can lead to conflicting conclusions regarding cortical excitation/inhibition ratio | Racz, F. S.; Mac-Auliffe, D.; Mukli, P.; Milton, J.; Cabrera, J. L.; Millan, J. d. R. | Frigyes Samuel Racz | The University of Texas at Austin | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622698.source.xml | Confluent recent evidence indicates that the spectral slope of 1/f neurophysiological recordings is correspondent to cortical excitation/inhibition (E/I) ratio. In this framework, a steeper power spectrum (i.e., one with a larger spectral exponent {beta}) is indicative of stronger inhibitory tone and thus lower E/I rat... | null | biorxiv |
10.1101/2024.11.08.622714 | The development of aperiodic neural activity in the human brain | Cross, Z. R.; Gray, S. M.; Dede, A. J. O.; Rivera, Y. M.; Yin, Q.; Vahidi, P.; Rau, E. M. B.; Cyr, C.; Holubecki, A. M.; Asano, E.; Lin, J. J.; McManus, O. K.; Sattar, S.; Saez, I.; Girgis, F.; King-Stephens, D.; Weber, P. B.; Laxer, K. D.; Schuele, S. U.; Rosenow, J. M.; Wu, J. Y.; Kam, S. K.; Raskin, J. S.; Chang, E.... | Zachariah Reuben Cross | Northwestern Feinberg School of Medicine, Northwestern University | 2024-11-09 | 1 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622714.source.xml | The neurophysiological mechanisms supporting brain maturation are fundamental to attention and memory capacity across the lifespan. Human brain regions develop at different rates, with many regions developing into the third and fourth decades of life. Here, in this preregistered study (https://osf.io/gsru7), we analyze... | null | biorxiv |
10.1101/2024.11.09.622780 | Can ERPs and neural oscillations be used to differentiate skilled and unskilled player performance in an ecologically valid sporting model? | Winstanley, M.; Drust, B. | Mike Winstanley | University of Birmingham, Centre for Human Brain Health | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622780.source.xml | The present study seeks to identify neural correlates of high performance in ecological valid, sporting tasks and quantify the differences between high skilled and low skilled players. To do this, Esports is chosen to be the sporting model to facilitate clean brain activity recordings whilst playing sport, something th... | null | biorxiv |
10.1101/2024.11.09.622778 | Anterior cingulate neurons display subregion-specific interaction with frontal eye fields as revealed by combined antidromic stimulation and resting state imaging | Babapoor-Farrokhran, S.; Major, A. J.; Johnston, K. D.; Miller, E. K.; Camprodon, J. A.; Everling, S. | Alex J. Major | The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA | 2024-11-09 | 1 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622778.source.xml | The anterior cingulate cortex (ACC) is thought to exert cognitive control over saccade generation in the frontal eye fields (FEF), but the nature of this interaction remains unclear. Although prior imaging studies have suggested ACC interacts with FEF, few studies have confirmed this by electrophysiological recordings.... | null | biorxiv |
10.1101/2024.11.09.622728 | Sex differences in central amygdala glutamate responses to calcitonin gene-related peptide | Lorsung, R.; Cramer, N.; Alipio, J. B.; Ji, Y.; Han, S.; Masri, R.; Keller, A. | Rebecca Lorsung | University of Maryland Baltimore | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622728.source.xml | Women are disproportionately affected by chronic pain compared to men. While societal and environmental factors contribute to this disparity, sex-based biological differences in the processing of pain are also believed to play significant roles. The central lateral nucleus of the amygdala (CeLC) is a key region for the... | null | biorxiv |
10.1101/2024.11.09.622275 | Retrospective Attention Can Trigger Visual Perception Without Dependence on Either Cue Awareness or Target Reporting | Li, Y.; Wan, X.; Mao, M.; Jin, L.; Zhang, X. | Ye Li | South China Normal University | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622275.source.xml | Retrospective attention, guided by cues after stimulus offset, enhances perception of threshold-level Gabor patches. The neural mechanisms underlying this effect, and its dependence on cue awareness and target reporting, remain unclear. Using EEG in report and no-report paradigms with visible and invisible post-cues, w... | null | biorxiv |
10.1101/2024.11.08.622733 | Medial prefrontal cortical neurotransmitters reactive to relapse-promoting and relapse-suppressing cues in rats trained to self-administer cocaine or alcohol | Nedelescu, H.; Miliano, C.; Wagner, G.; Kerr, T.; Gregus, A.; Weiss, F.; Buczynski, M.; Suto, N. | Nobuyoshi Suto | Mayo Clinic | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622733.source.xml | Environmental cues conditioned to signal drug availability (S+) or omission (S-) activate specific neurons (neuronal ensembles/engram cells) within the medial prefrontal cortex (mPFC) to promote and suppress drug relapse in rats. However, the neurochemical source of such cue-specific activation remains unknown. In this... | null | biorxiv |
10.1101/2024.11.07.622553 | Neural Context Reinstatement of Recurring Events | Broitman, A. W.; Kahana, M. J. | Adam W. Broitman | University of Pennsylvania | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622553.source.xml | Episodic recollection involves retrieving context information bound to specific events. However, autobiographical memory largely comprises recurrent, similar experiences that become integrated into joint representations. In the current study, we extracted a neural signature of temporal context from scalp electroencepha... | null | biorxiv |
10.1101/2024.11.09.622721 | A Neural Network Model of Visual Attention Integrating Biased Competition and Reinforcement Learning | Morgan, J. M.; Albanna, B.; Herman, J. P. | James P Herman | University of Pittsburgh | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622721.source.xml | We present a neural network model of visual attention (NNMVA) that integrates biased competition and reinforcement learning to capture key aspects of attentional behavior. The model combines self-attention mechanisms from Vision Transformers (ViTs), Long Short-Term Memory (LSTM) networks for working memory, and an acto... | null | biorxiv |
10.1101/2024.11.08.622602 | Pathogenesis and immune response to respiratory coronaviruses in their natural porcine host | Sedaghat-Rostami, E.; Carr, B. V.; Yang, L.; Keep, S.; Lean, F. Z. X.; Atkinson, I.; Fones, A.; Paudyal, B.; Kirk, J.; Vatzia, E.; Gubbins, S.; Bickerton, E.; Briggs, E.; Nunez, A. Z. X.; MacNee, A.; Moffat, K.; Freimanis, G.; Rollier, C.; Muir, A.; Richard, A. C.; Angelopoulos, N.; Gerner, W.; Tchilian, E. | Elma Tchilian | Pirbright Institute | 2024-11-09 | 1 | new results | cc_by | immunology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622602.source.xml | Porcine respiratory coronavirus (PRCV) is a naturally occurring pneumotropic coronavirus in the pig, providing a valuable large animal model to study acute respiratory disease. PRCV pathogenesis and the resulting immune response was investigated in pigs, the natural large animal host. We compared two strains, ISU-1 and... | null | biorxiv |
10.1101/2024.11.09.622705 | Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance in Candida albicans | Obermeier, M.; Esparza Mora, M. A.; Heese, O.; Cohen, N.; Varma, S. J.; Tober-Lau, P.; Hartl, J.; Kurth, F.; Berman, J.; Ralser, M. | Markus Ralser | Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622705.source.xml | Background Fungal infections are an increasing concern, particularly among immunocompromised patients and those with comorbidities who require multiple medications. However, the effects of drugs targeting human pathways on fungal cells, and whether they influence antifungal drug responses, are poorly understood. Method... | null | biorxiv |
10.1101/2024.11.08.622737 | Drospondin, a novel glial-secreted glycoprotein, controls the development and function of the Drosophila nervous system | Rojo-Cortes, F.; Roa-Siegfried, C.; Fuenzalida-Uribe, N.; Amado-Hinojosa, P.; Gonzalez-Ramirez, M.-C.; Almonacid-Torres, I.; Birman, S.; Goodman, L. D.; Kanka, O.; Oliva, C.; Marzolo, M.-P.; Campusano, J. M. | Jorge M Campusano | Pontificia Universidad Católica de Chile | 2024-11-09 | 1 | new results | cc_no | developmental biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622737.source.xml | Reelin is a secreted glycoprotein with roles in the development of the mammalian hippocampus and cerebral cortex. This vertebrate signaling molecule also contributes to adult brain function. Mammalian Reelin increases the complexity of Drosophila Mushroom Body (MB) neurites, an effect mediated by LpR1 and LpR2, the ort... | null | biorxiv |
10.1101/2024.11.07.622474 | Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation | Dong, Z.; Schaffner, S.; Fu, M.; Whitehead, J.; MacIsaac, J. L.; Rehkopf, D. H.; Boyce, W. T.; Rosero-Bixby, L.; Quintana-Murci, L.; Patin, E.; Miller, G. E.; Korthauer, K.; Kobor, M. S. | Michael S. Kobor | University of British Columbia | 2024-11-09 | 1 | new results | cc_by_nc | genetics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622474.source.xml | DNA methylation (DNAm) is a key epigenetic mark that modulates regulatory elements and gene expression, playing a crucial role in mammalian development and physiological function. Despite extensive characterization of DNAm profiles across species, little is known about its evolutionary conservation. Here, we conducted ... | null | biorxiv |
10.1101/2024.11.09.622763 | Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation | Kulkarni, O.; Mathew, R. J.; Zaveri, L.; Jana, R.; Singh, N. K.; Ara, S.; Tallapaka, K. B.; Sowpati, D. T. | Divya Tej Sowpati | CSIR Centre for Cellular and Molecular Biology | 2024-11-09 | 1 | new results | cc_by_nd | genomics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622763.source.xml | Long read sequencing technologies such as Oxford Nanopore (ONT) offer direct detection of DNA base modifications. While several tools and models have been developed to identify DNA methylation from nanopore data, they are often restricted to 5-methylcytosine (5mC) and older flowcell (FC) chemistry. The performance and ... | null | biorxiv |
10.1101/2024.11.08.622731 | Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 | Martin, A.; Arkinson, C.; Gee, C. L.; Zhang, Z.; Dong, K. | Andreas Martin | HHMI, UC Berkeley | 2024-11-09 | 1 | new results | cc_by_nc_nd | biochemistry | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622731.source.xml | The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting cofactors thereby modulates these functions and aids in substrate degradation. Here, we solved several high-resolution str... | null | biorxiv |
10.1101/2024.11.09.622779 | DnaB and DciA: Mechanisms of Helicase Loading and Translocation on ssDNA | Gao, N.; Mazzoletti, D.; Peng, A.; Olinares, P. D. B.; Morrone, C.; Garavaglia, A.; Gouda, N.; Tsoy, S.; Mendoza, A.; Chowdhury, A.; Cerullo, A. R.; Bhavsar, H.; Rossi, F.; Rizzi, M.; Chait, B.; Miggiano, R.; Jeruzalmi, D. | David Jeruzalmi | Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA. Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduat | 2024-11-09 | 1 | new results | cc_no | biochemistry | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622779.source.xml | Replicative helicases are assembled on chromosomes by helicase loaders before initiation of DNA replication. Here, we investigate mechanisms used by the bacterial DnaB replicative helicase and the DciA helicase loader. In the present structure of the DnaB-ssDNA-ATP-gamma-S complex, the amino-terminal (NTD) tier, previo... | null | biorxiv |
10.1101/2024.11.09.622773 | Crystal structure of plant γ-glutamyl peptidase 1 with dual roles in sulfur metabolism and implications for oxidative stress regulation | Sone, K.; Ito, T.; Yamada, C.; Kashima, T.; Miyanaga, A.; Ohkama-Ohtsu, N.; Fushinobu, S. | Shinya Fushinobu | Department of Biotechnology, The University of Tokyo | 2024-11-09 | 1 | new results | cc_no | biochemistry | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622773.source.xml | {gamma}-Glutamyl peptidase 1 (GGP1) plays a dual role in primary and secondary sulfur metabolism in Arabidopsis thaliana. During glutathione (GSH) turnover, GGP1 hydrolyzes the isopeptide bond of GSH to degrade the tripeptide into Glu and Cys-Gly. During glucosinolate and camalexin biosynthesis, GGP1 processes GSH conj... | null | biorxiv |
10.1101/2024.11.07.622410 | Language model generates cis-regulatory elements across prokaryotes | Xia, Y.; Sun, J.; Du, X.; Liang, Z.; Shi, W.; Guo, S.; Huo, Y.-X. | Yi-Xin Huo | Beijing Institute of Technology | 2024-11-09 | 1 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622410.source.xml | Deep learning had succeeded in designing Cis-regulatory elements (CREs) for certain species, but necessitated training data derived from experiments. Here, we present Promoter-Factory, a protocol that leverages language models (LM) to design CREs for prokaryotes without experimental prior. Millions of sequences were dr... | null | biorxiv |
10.1101/2024.11.07.622529 | RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling | Lim, C. S.; Brown, C. | Chun Shen Lim | University of Otago | 2024-11-09 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622529.source.xml | Ribosome profiling is a high-throughput sequencing technique that captures the positions of translating ribosomes on RNAs. Recent advancements in ribosome profiling include achieving highly-phased ribosome footprints for plant translatomes and more recently for bacterial translatomes. This substantially increases the s... | null | biorxiv |
10.1101/2024.11.07.622480 | Computational Modeling and Analysis of the TGF-β-induced ERK and SMAD Pathways | Chung, S.; Cooper, C. R.; Farach-Carson, M. C.; Ogunnaike, B. A. | Mary C. Farach-Carson | University of Texas Health Science Center at Houston School of Dentistry | 2024-11-09 | 1 | new results | cc_by_nc_nd | systems biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622480.source.xml | Transforming growth factor-{beta} (TGF-{beta}), an important cytokine that plays a key role in many diseases regulates a wide array of cellular and physiologic processes via several TGF-{beta}-driven signaling cascades, including the SMAD and non-SMAD-driven pathways. However, the detailed mechanisms by which TGF-{beta... | null | biorxiv |
10.1101/2024.11.07.622236 | Translocation of gut Enterococcus faecalis trains myeloid bone marrow progenitors via the C-type lectin receptor Mincle | Robles-Vera, I.; Sancho, D. | David Sancho | Centro Nacional de Investigaciones Cardiovasculares | 2024-11-09 | 1 | new results | cc_by_nc_nd | immunology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622236.source.xml | Impairment of the intestinal barrier allows the systemic translocation of commensal bacteria, inducing a pro-inflammatory state in the host. To address potential mechanisms underlying this link, we explored innate immune responses following increased gut permeability upon administration of dextran sulfate sodium (DSS) ... | null | biorxiv |
10.1101/2024.11.08.621386 | Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism | Woo, A. Y. M.; Sandoval-Espinola, W. J.; Bollenbach, M.; Wong, A.; Sakanaka-Yokoyama, M.; Zhang, Q.; Nieto, V.; Rey, F. E.; Balskus, E. P. | Emily P. Balskus | Harvard University | 2024-11-09 | 1 | new results | cc_by | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.621386.source.xml | Anaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The host's impaired ability to oxidize TMA to trimethylamine-N-oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabo... | null | biorxiv |
10.1101/2024.11.08.622732 | Commonalities and differences in the Cryptococcus neoformans response to ingestion by protozoal and mammalian phagocytic cells suggests host cell metabolism as a target for intracellular survival | Dragotakes, Q.; Jacobs, E.; Gerbig, G.; Greengo, S.; Jedlicka, A.; Dziedzic, A.; Casadevall, A. | Quigly Dragotakes | Johns Hopkins | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622732.source.xml | The outcome of the interaction between Cryptococcus neoformans and infected hosts can be determined by whether the fungal cell survives ingestion by phagocytic cells. This applies to both unicellular and multicellular hosts such as amoeba and animals, respectively. Ingestion by phagocytic cells results in the formation... | null | biorxiv |
10.1101/2024.11.08.622711 | Microbial Differences Accurately Identifies Global SERT KO Phenotype in Mice | Leitman, M.; Katza, W.; Zhang, D.; Pawar, S.; Shera, S.; Hernandez, L.; Dong, T. | Tien Dong | University of California, Los Angeles | 2024-11-09 | 1 | new results | cc_by_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622711.source.xml | Altered serotonin signaling is a well-established contributor to depression, with the serotonin transporter gene (SERT) playing a critical role in regulating serotonin reuptake. Mice lacking SERT (SERT -/-) serve as a robust model for depression, exhibiting significant depressive-like behaviors compared to littermate w... | null | biorxiv |
10.1101/2024.11.08.622677 | Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter? | Nickols, W. A.; McIver, L. J.; Walsh, A.; Zhang, Y.; Nearing, J.; Asnicar, F.; Nguyen, L.; Hartmann, E. M.; Franzosa, E. A.; Huttenhower, C.; Thompson, K. N. | Kelsey N. Thompson | Harvard University | 2024-11-09 | 1 | new results | cc_by | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622677.source.xml | Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed sim... | null | biorxiv |
10.1101/2024.11.09.622791 | Isolation, Characterization, and Identification of Nitrogen Fixing Bacteria from Rhizosphere of Sonneratia apetala Collected from Sundarbans | Rimi, A. A.; Roshnee, F. I.; Shuvro, K.; Tasin, M. H. R.; Akter, R.; Islam, M. E.; Islam, K. M. D.; Rahman, S. M. M.; Billah, M. M. | Md Morsaline Billah | Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622791.source.xml | Nitrogen is a crucial element for plant growth, driving vibrant greenery, photosynthesis, and overall vitality. This research focused on isolating, characterizing, and identifying nitrogen-fixing bacteria from the rhizosphere of Sonneratia apetala in the Sundarbans, Khulna, Bangladesh, with the goal of assessing their ... | null | biorxiv |
10.1101/2024.11.08.622696 | Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mtDNA copy number in songbird blood and sperm cells | Bagdonaite, L.; Leder, E. H.; Lifjeld, J. T.; Johnsen, A.; Mauvisseau, Q. | Laima Bagdonaite | Natural History Museum, University of Oslo | 2024-11-09 | 1 | new results | cc_by_nc_nd | molecular biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622696.source.xml | Mitochondrial DNA copy number varies across species, individuals and cell types. Two avian cell types carrying a relatively low number of mitochondria are the red blood cells and spermatozoa. While previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (... | null | biorxiv |
10.1101/2024.11.09.622792 | Perilipin 5 Phosphorylation is Dispensable for Upregulation of Hepatic Lipid Metabolism Genes upon Fasting but Required for Insulin Receptor Substrate 2 Expression in Male Mice | Bovee, C.; Grandgenett, R.; Trevino, M.; Dutta, S.; Peachee, S.; Kopriva, S.; Haider, F.; Liu, S.; Bhardwaj, G.; Penniman, C.; O'Neill, B.; Imai, Y. | Yumi Imai | University of Iowa | 2024-11-09 | 1 | new results | cc_no | molecular biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622792.source.xml | Objective Perilipin 5 (PLIN5) is a lipid droplet protein highly expressed in cells that actively oxidize fatty acids. Previous in vitro studies have revealed that PLIN5 phosphorylation (p-PLIN5) at serine 155 by PKA is critical for transcriptional regulation of PPARa target genes by which PLIN5 adapt cells for fatty ac... | null | biorxiv |
10.1101/2024.11.07.622440 | Unpacking fitness differences between two invaders in a multispecies context | Freire, T. F. A.; Madec, S.; Gjini, E. | Erida Gjini | Center for Computational and Stochastic Mathematics, Instituto Superior Tecnico, University of Lisbon, Lisbon, Portugal | 2024-11-09 | 1 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622440.source.xml | Ecosystems are constantly exposed to new strains of a given species. Which strain will be able to invade a resident multi-species community depends on the strain's relative fitness. Here we develop an approach to quantify fitness differences between two co-invading strains based on the replicator equation. By assuming ... | null | biorxiv |
10.1101/2024.11.08.622685 | Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes | Stevenson, Z. C.; Laufer, E.; Estevez, A. O.; Robinson, K.; Phillips, P. C. | Patrick C. Phillips | University of Oregon | 2024-11-09 | 1 | new results | cc_by_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622685.source.xml | A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted t... | null | biorxiv |
10.1101/2024.11.07.622307 | A consensus variant-to-function score to functionally prioritize variants for disease | Fabiha, T.; Raine, I.; Kundu, S.; Pampari, A.; Abramov, S.; Boytsov, A.; Strouse, K.; Dura, K.; Fang, W.; Kerner, G.; Butts, J.; Ali, T.; Gschwind, A.; Mualim, K. S.; Moore, J. E.; Weng, Z.; Ulirsch, J.; Ji, H. E.; Vierstra, J.; Reddy, T. E.; Montgomery, S. B.; Engreitz, J.; Kundaje, A.; Tewhey, R.; Price, A.; Dey, K. | Kushal Dey | Memorial Sloan Kettering Cancer Center; Weill Cornell Medicine | 2024-11-09 | 1 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622307.source.xml | Identifying and functionally characterizing causal disease variants in genome-wide association studies remains a pressing challenge. Here, we construct a consensus variant-to-function (cV2F) score that assigns a single value to each common single-nucleotide variant in the genome, and helps to predict and characterize c... | null | biorxiv |
10.1101/2024.11.07.622307 | A consensus variant-to-function score to functionally prioritize variants for disease | Fabiha, T.; Evergreen, I.; Kundu, S.; Pampari, A.; Abramov, S.; Boytsov, A.; Strouse, K.; Dura, K.; Fang, W.; Kerner, G.; Butts, J.; Ali, T.; Gschwind, A.; Mualim, K. S.; Moore, J. E.; Weng, Z.; Ulirsch, J.; Ji, H. E.; Vierstra, J.; Reddy, T. E.; Montgomery, S. B.; Engreitz, J.; Kundaje, A.; Tewhey, R.; Price, A.; Dey,... | Kushal Dey | Memorial Sloan Kettering Cancer Center; Weill Cornell Medicine | 2024-11-10 | 2 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/10/2024.11.07.622307.source.xml | Identifying and functionally characterizing causal disease variants in genome-wide association studies remains a pressing challenge. Here, we construct a consensus variant-to-function (cV2F) score that assigns a single value to each common single-nucleotide variant in the genome, and helps to predict and characterize c... | null | biorxiv |
10.1101/2024.11.08.622724 | Generation of a novel constitutive smooth muscle cell-specific Myh11-driven Cre mouse model | Dong, K.; Bai, Z.; He, X.; Zhang, L.; Hu, G.; Yao, Y.; Cai, C.-L.; Zhou, J. | Jiliang Zhou | https://www.augusta.edu/ | 2024-11-09 | 1 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622724.source.xml | Dysfunction in either embryonic or postnatal vascular smooth muscle cells (SMCs) significantly contributes to the progression of various cardiovascular diseases. Therefore, elucidating the molecular mechanisms governing VSMC development and homeostasis is crucial. MYH11 is the most reliable lineage gene for SMCs and ha... | null | biorxiv |
10.1101/2024.11.07.622479 | TissueMosaic enables cross-sample differential analysis of spatial transcriptomics datasets through self-supervised representation learning | Kambhampati, S.; D'Alessio, L.; Grab, F.; Fleming, S. J.; Chen, F.; Babadi, M. | Sandeep Kambhampati | Harvard University | 2024-11-09 | 1 | new results | cc_no | bioinformatics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622479.source.xml | Spatial transcriptomics allows for the measurement of gene expression within native tissue context, thereby improving our understanding of how cell states are modulated by their microenvironment. Despite technological advancements, computational methods to link cell states with their microenvironment and perform compar... | null | biorxiv |
10.1101/2024.11.06.622264 | Phenylacetic acid metabolism in land plants: novel pathways and metabolites | Hladik, P.; Brunoni, F.; Zukauskaite, A.; Zatloukal, M.; Belicek, J.; Kopecny, D.; Briozzo, P.; Ferchaud, N.; Novak, O.; Pencik, A. | Ales Pencik | Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacky University, Olomouc, Czech Republ | 2024-11-09 | 1 | new results | cc_by | plant biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.06.622264.source.xml | In recent years, substantial progress has been made in exploring auxin conjugation and metabolism, primarily aiming at indole-3-acetic acid (IAA). However, the metabolic regulation of another key auxin, phenylacetic acid (PAA), remains largely uncharacterized. Here, we provide a comprehensive exploration of PAA metabol... | null | biorxiv |
10.1101/2024.11.08.622749 | Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display | Wang, S.; Faucher, F. F.; Bertolini, M.; Kim, H.; Yu, B.; Cao, L.; Roeltgen, K.; Lovell, S.; Shanker, V.; Boyd, S. D.; Wang, L.; Bartenschlager, R.; Bogyo, M. | Matthew Bogyo | Stanford University | 2024-11-09 | 1 | new results | cc_by_nc_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622749.source.xml | Peptide macrocycles are promising therapeutics for a variety of disease indications due to their overall metabolic stability and potential to make highly selective binding interactions with targets. Recent advances in covalent macrocycle peptide discovery, driven by phage and mRNA display methods, have enabled the rapi... | null | biorxiv |
10.1101/2024.11.08.622755 | Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating | Fujiwara, T.; Hosaka, T.; Hasegawa-Takano, M.; Nishimura, Y.; Tominaga, K.; Mori, K.; Nishino, S.; Takahashi, Y.; Uchikubo-Kamo, T.; Hanada, K.; Maoka, T.; Takaichi, S.; Inoue, K.; Shirouzu, M.; Yoshizawa, S. | Susumu Yoshizawa | The University of Tokyo | 2024-11-09 | 1 | new results | cc_by_nc_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622755.source.xml | Microbial rhodopsins, photoreceptor proteins widely distributed in marine microorganisms, receive large amount of light energy that sustains marine ecosystems. Although rhodopsins generally harbor retinal as their only chromophore, a recent study reported that carotenoid antennae transfer light energy to the retinal in... | null | biorxiv |
10.1101/2024.11.08.622053 | A bacterial cell wall repair and modification system to resist host antibacterial factors | Burnier, J.; Gallay, C.; Bruce, K.; Bjanes, E.; Martin, L.; Jim, K. K.; Tsui, T.; Cremers, A.; Mignolet, J.; Vollmer, D.; Biboy, J.; Nizet, V.; Vollmer, W.; Winkler, M. E.; Veening, J.-W. | Jan-Willem Veening | University of Lausanne | 2024-11-09 | 1 | new results | cc_by | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622053.source.xml | Pathogenic bacteria have acquired the ability to resist antibacterial defense mechanisms of the host. Streptococci are common in animal microbiota and include opportunistic pathogens like Group A Streptococcus (GAS) and Streptococcus pneumoniae (pneumococcus). While the conserved streptococcal S protein has been identi... | null | biorxiv |
10.1101/2024.11.09.622756 | Characterization of a GpsB-associated regulator of PBP1a reveals the organization of the cell wall remodeling complex of Streptococcus pneumoniae | Millat, H.; Lenoir, C.; Falcou, C.; Cluzel, C.; Zapun, A.; Roper, D.; Morlot, C.; Ducret, A.; Grangeasse, C. | Christophe Grangeasse | Universite de Lyon/CNRS | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622756.source.xml | Class A PBPs (aPBPs) play a key role in the biosynthesis and remodeling of peptidoglycan, the main component of the bacterial cell wall. The human bacterial pathogen Streptococcus pneumoniae produces three aPBPs, which are regulated to maintain the bacterium ovoid shape. Although their exact functions remain unclear, e... | null | biorxiv |
10.1101/2024.11.07.622502 | Bayesian nonparametric analysis of residence times for protein-lipid interactions in Molecular Dynamics simulations | Sexton, R. C.; Fazel, M.; Schweiger, M. C.; Presse, S.; Beckstein, O. | Oliver Beckstein | Arizona State University | 2024-11-09 | 1 | new results | cc_by | biophysics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622502.source.xml | Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid-protein binding kinetics has remained challenging due to considerable noise and low freq... | null | biorxiv |
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